Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.14 kDa 
• Atom Count: 5206 
• Residue Count: 598 
• Unique protein chains: 1

2YKO

Structure of the human LINE-1 ORF1p trimer

• DOI: 10.2210/pdb2YKO/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-05-28 Released: 2011-08-10 
• Deposition Author(s): Khazina, E., Weichenrieder, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Trimeric Structure and Flexibility of the L1Orf1P Protein in Human L1 Retrotransposition

Khazina, E., Truffault, V., Buettner, R., Schmidt, S., Coles, M., Weichenrieder, O.

(2011) Nat Struct Mol Biol 18: 1006

• PubMed: 21822284 
• DOI: 10.1038/nsmb.2097
• Primary Citation of Related Structures:  
  2LDY, 2YKO, 2YKP, 2YKQ


• PubMed Abstract: 
  

The LINE-1 (L1) retrotransposon emerges as a major source of human interindividual genetic variation, with important implications for evolution and disease. L1 retrotransposition is poorly understood at the molecular level, and the mechanistic details and evolutionary origin of the L1-encoded L1ORF1 protein (L1ORF1p) are particularly obscure. Here three crystal structures of trimeric L1ORF1p and NMR solution structures of individual domains reveal a sophisticated and highly structured, yet remarkably flexible, RNA-packaging protein. It trimerizes via an N-terminal, ion-containing coiled coil that serves as scaffold for the flexible attachment of the central RRM and the C-terminal CTD domains. The structures explain the specificity for single-stranded RNA substrates, and a mutational analysis indicates that the precise control of domain flexibility is critical for retrotransposition. Although the evolutionary origin of L1ORF1p remains unclear, our data reveal previously undetected structural and functional parallels to viral proteins.

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Organizational Affiliation: 

Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LINE-1 ORF1P	A, B, C	233	Homo sapiens	Mutation(s): 5  Gene Names: L1RE1, LRE1
Find proteins for Q9UN81 (Homo sapiens) Explore Q9UN81  Go to UniProtKB:  Q9UN81

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B,C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.69	α = 90
b = 85.42	β = 90
c = 111.45	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SHELX	phasing
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-28 
• Released Date: 2011-08-10 
Deposition Author(s): Khazina, E., Weichenrieder, O.

Revision History 

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Atomic model, Database references, Derived calculations, Other
• Version 1.2: 2011-09-14
  Changes: Database references
• Version 1.3: 2012-10-10
  Changes: Database references